FMO DATABASE

FMODB ID: 3J31L

Calculation Name: 2Q8R-E-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2Q8R

Chain ID: E

ChEMBL ID:

UniProt ID: Q16627

Base Structure: X-ray

Registration Date: 2023-09-20

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	64
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-393574.009993
FMO2-HF: Nuclear repulsion	365064.776824
FMO2-HF: Total energy	-28509.233168
FMO2-MP2: Total energy	-28588.247997

3D Structure

Snapshot

Ligand structure

Ligand Interaction

Ligand binding energy

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
N/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(E:1:GLY)

Summations of interaction energy for fragment #1(E:1:GLY)

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
4.127	6.146	0.002	-0.995	-1.025	0.002

Interaction energy analysis for fragmet #1(E:1:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.079 / q_NPA : 0.039

Distance from base fragment(s) [Å]

Dist

Interaction energy by IFIE and PIEDA
[kcal/mol]

| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >

Fragment charge [e]

FCHARGE q_Mulliken
q_NPA q(I=>J)

Residue

Res # RES

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Graph Options

X Axis Label
Y Axis Max Y Axis Min
Display ES EX CT+mix DI(MP2)

frag_NumFragment number.	ChainChain species.	Res #Residue number.	RES3-letter code of amino acid residue, ligand and solvent molecule.	FCHARGEFormal charge [e].	q_MullikenFragment charge evaluated by Mulliken charge [e].	q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e].	DISTDistance from Ligand [Å].	TotalIFIE at MP2 level [kcal/mol].	ESElectro static interaction energy by PIEDA [kcal/mol].	EXExchange-repulsion energy by PIEDA [kcal/mol].	CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol].	DI(MP2)Dispersion energy by PIEDA [kcal/mol].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	E	3	TYR	0	0.005	-0.003	3.629	-0.394	1.323	0.001	-0.878	-0.839	0.002
4	E	4	HIS	1	0.873	0.952	3.772	4.839	5.141	0.001	-0.117	-0.186	0.000
5	E	5	PRO	0	0.070	0.033	5.626	0.271	0.271	0.000	0.000	0.000	0.000
6	E	6	SER	0	-0.015	-0.011	8.806	-0.313	-0.313	0.000	0.000	0.000	0.000
7	E	7	GLU	-1	-0.879	-0.922	11.562	-0.585	-0.585	0.000	0.000	0.000	0.000
8	E	8	CYS	0	-0.061	-0.031	14.646	-0.016	-0.016	0.000	0.000	0.000	0.000
9	E	9	CYS	0	0.025	0.037	17.966	0.021	0.021	0.000	0.000	0.000	0.000
10	E	10	PHE	0	0.066	0.033	18.988	0.027	0.027	0.000	0.000	0.000	0.000
11	E	11	THR	0	-0.038	-0.006	23.715	0.019	0.019	0.000	0.000	0.000	0.000
12	E	12	TYR	0	0.004	-0.029	24.365	-0.008	-0.008	0.000	0.000	0.000	0.000
13	E	13	THR	0	-0.030	-0.011	27.433	0.018	0.018	0.000	0.000	0.000	0.000
14	E	14	THR	0	0.039	0.014	29.779	-0.005	-0.005	0.000	0.000	0.000	0.000
15	E	15	TYR	0	-0.058	-0.019	32.587	0.010	0.010	0.000	0.000	0.000	0.000
16	E	16	LYS	1	0.979	0.995	32.013	0.104	0.104	0.000	0.000	0.000	0.000
17	E	17	ILE	0	0.025	0.024	26.973	0.009	0.009	0.000	0.000	0.000	0.000
18	E	18	PRO	0	-0.009	-0.005	31.316	0.002	0.002	0.000	0.000	0.000	0.000
19	E	19	ARG	1	0.904	0.937	30.898	0.106	0.106	0.000	0.000	0.000	0.000
20	E	20	GLN	0	0.059	0.035	30.379	-0.009	-0.009	0.000	0.000	0.000	0.000
21	E	21	ARG	1	0.901	0.939	28.977	0.113	0.113	0.000	0.000	0.000	0.000
22	E	22	ILE	0	-0.013	0.000	25.022	-0.003	-0.003	0.000	0.000	0.000	0.000
23	E	23	MET	0	-0.070	-0.027	22.788	0.023	0.023	0.000	0.000	0.000	0.000
24	E	24	ASP	-1	-0.801	-0.892	18.263	-0.248	-0.248	0.000	0.000	0.000	0.000
25	E	25	TYR	0	-0.068	-0.049	20.545	0.010	0.010	0.000	0.000	0.000	0.000
26	E	26	TYR	0	0.057	0.040	15.700	-0.035	-0.035	0.000	0.000	0.000	0.000
27	E	27	GLU	-1	-0.933	-0.970	17.230	-0.335	-0.335	0.000	0.000	0.000	0.000
28	E	28	THR	0	-0.037	-0.025	16.166	-0.051	-0.051	0.000	0.000	0.000	0.000
29	E	29	ASN	0	0.004	-0.016	12.116	0.130	0.130	0.000	0.000	0.000	0.000
30	E	30	SER	0	0.033	0.012	15.128	0.028	0.028	0.000	0.000	0.000	0.000
31	E	31	GLN	0	0.001	0.006	12.941	-0.074	-0.074	0.000	0.000	0.000	0.000
32	E	33	SER	0	-0.009	-0.007	18.644	0.026	0.026	0.000	0.000	0.000	0.000
33	E	34	LYS	1	0.836	0.914	21.799	0.308	0.308	0.000	0.000	0.000	0.000
34	E	35	PRO	0	0.058	0.037	21.624	-0.033	-0.033	0.000	0.000	0.000	0.000
35	E	36	GLY	0	0.022	0.006	21.400	0.032	0.032	0.000	0.000	0.000	0.000
36	E	37	ILE	0	0.014	0.034	20.654	-0.033	-0.033	0.000	0.000	0.000	0.000
37	E	38	VAL	0	0.001	-0.007	18.543	0.030	0.030	0.000	0.000	0.000	0.000
38	E	39	PHE	0	0.015	0.008	20.445	-0.004	-0.004	0.000	0.000	0.000	0.000
39	E	40	ILE	0	0.038	0.025	16.879	0.004	0.004	0.000	0.000	0.000	0.000
40	E	41	THR	0	-0.035	-0.039	21.385	0.031	0.031	0.000	0.000	0.000	0.000
41	E	42	LYS	1	0.900	0.930	23.501	0.078	0.078	0.000	0.000	0.000	0.000
42	E	43	ARG	1	0.892	0.942	25.065	0.089	0.089	0.000	0.000	0.000	0.000
43	E	44	GLY	0	0.047	0.041	20.744	0.005	0.005	0.000	0.000	0.000	0.000
44	E	45	HIS	0	0.006	0.006	19.979	-0.041	-0.041	0.000	0.000	0.000	0.000
45	E	46	SER	0	0.033	0.024	18.759	-0.006	-0.006	0.000	0.000	0.000	0.000
46	E	47	VAL	0	-0.037	-0.022	21.025	0.002	0.002	0.000	0.000	0.000	0.000
47	E	49	THR	0	-0.050	-0.040	23.470	0.035	0.035	0.000	0.000	0.000	0.000
48	E	50	ASN	0	0.060	0.031	25.056	-0.039	-0.039	0.000	0.000	0.000	0.000
49	E	51	PRO	0	0.049	0.022	23.918	0.016	0.016	0.000	0.000	0.000	0.000
50	E	52	SER	0	-0.004	-0.009	26.646	0.017	0.017	0.000	0.000	0.000	0.000
51	E	53	ASP	-1	-0.824	-0.893	30.139	-0.151	-0.151	0.000	0.000	0.000	0.000
52	E	54	LYS	1	0.869	0.920	31.179	0.115	0.115	0.000	0.000	0.000	0.000
53	E	55	TRP	0	-0.020	-0.030	29.468	0.002	0.002	0.000	0.000	0.000	0.000
54	E	56	VAL	0	0.027	0.022	26.520	0.003	0.003	0.000	0.000	0.000	0.000
55	E	57	GLN	0	-0.003	-0.009	28.229	0.005	0.005	0.000	0.000	0.000	0.000
56	E	58	ASP	-1	-0.851	-0.921	29.758	-0.121	-0.121	0.000	0.000	0.000	0.000
57	E	59	TYR	0	-0.098	-0.075	28.329	0.011	0.011	0.000	0.000	0.000	0.000
58	E	60	ILE	0	0.035	0.020	24.445	0.005	0.005	0.000	0.000	0.000	0.000
59	E	61	LYS	1	0.929	0.969	26.836	0.112	0.112	0.000	0.000	0.000	0.000
60	E	62	ASP	-1	-0.845	-0.911	29.610	-0.102	-0.102	0.000	0.000	0.000	0.000
61	E	63	MET	0	-0.081	-0.024	24.096	0.006	0.006	0.000	0.000	0.000	0.000
62	E	64	LYS	1	0.884	0.951	24.174	0.166	0.166	0.000	0.000	0.000	0.000
63	E	65	GLU	-1	-0.886	-0.923	25.845	-0.083	-0.083	0.000	0.000	0.000	0.000
64	E	66	ASN	0	-0.036	-0.023	26.801	-0.012	-0.012	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(E:1:GLY)